if you have a diy adapter that is probably the problem. there has to be a buffer chip on some of the pins or the denise? chip will think it is hooked to a genlock and will not initialize properly.
there are several adapters on aminet that have the chip properly setup. a simple straight through adapter is simpler but it wont work.
i had an nec 3d multisync with the original commodore adapter and it worked perfectly.
Different revisions of the chips act slightly differently with some devices.